GapMind for catabolism of small carbon sources

 

Aligments for a candidate for deoB in Sinorhizobium meliloti 1021

Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate SMc00637 SMc00637 phosphoglucosamine mutase

Query= BRENDA::Q6I7B6
         (450 letters)



>lcl|FitnessBrowser__Smeli:SMc00637 SMc00637 phosphoglucosamine
           mutase
          Length = 450

 Score =  168 bits (426), Expect = 3e-46
 Identities = 142/447 (31%), Positives = 227/447 (50%), Gaps = 51/447 (11%)

Query: 2   RLFGTAGIRG-TLWEKVTPELAMKVGMAVGT-YKSG----KALVGRDGRTSSVMLKNAMI 55
           R FGT GIRG +    +TP+LAM+VG+AVGT +++G    + ++G+D R S  ML+NAM+
Sbjct: 4   RYFGTDGIRGQSNIFPMTPDLAMRVGIAVGTIFRNGAHRHRVVIGKDTRLSGYMLENAMV 63

Query: 56  SGLLSTGMEVLDADLIPTPALAWGTRKL-ADAGVMITASHNPPTDNGVKVFNGDGTEFYV 114
           +G  + G++V     IPTP +A  TR L AD GVMI+ASHN   DNG+K+F  DG +   
Sbjct: 64  AGFTAAGLDVFLLGPIPTPGVAMLTRSLRADIGVMISASHNAFRDNGIKLFGPDGYKLSD 123

Query: 115 EQERGLEEII---FSGNFRKARWDEIKPVRNVEV-IPDYINAVLDFVGHETNLK---VLY 167
           + E+ +E+++    SG   K   ++I   + V+  I  YI      +  +  LK   +  
Sbjct: 124 DIEQKIEDLLEQDMSGQLAKP--EDIGRAKRVDGDIYRYIEQAKRTLPRDVTLKGLRIAI 181

Query: 168 DGANGAGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVDLA 227
           D ANGA   VAP  L E+GA+V+++    +G       E    + A L K V E+  D+ 
Sbjct: 182 DCANGAAYKVAPSALWELGAEVVTIGTEPNG--VNINLECGSTHPAALQKKVHEVRADIG 239

Query: 228 IAQDGDADRIAVFDEKGNYVDEDTVIALFAKLYVEEH--GGGTVVVSIDTGSRIDAVVER 285
           IA DGDADR+ + DE+G  +D D ++A+ A  +  +    GG +  ++ +   ++  ++ 
Sbjct: 240 IALDGDADRVLIVDEEGAVIDGDQLMAVIADSWAADGMLKGGGIAATVMSNLGLERYLQA 299

Query: 286 AGGRVVRIPLGQPH-------DGIKRYKAIFAAEPWKLVHPKFGPWIDPFVTMGLLIKLI 338
              ++ R  +G  +       DG+     +   +   +V   FG   D  V    ++ ++
Sbjct: 300 RRLKLHRTKVGDRYVVEQMRQDGLN----VGGEQSGHIVLSDFGTTGDGLVAALQILAVV 355

Query: 339 DENG-PLSELVK--EIPTYYLKKANVLCPDEYKAEVVRRAAEEVERKLSSEIKEVLTISG 395
              G  +SE+ +  E     LK   V      +   V++A  E E +L+   +       
Sbjct: 356 KRQGKTVSEICRRFEPVPQVLKNVRVSAGKPLEDAAVQQAIAEAEAQLAKNGR------- 408

Query: 396 FRIALNDGSWILIRPSGTEPKIRVVAE 422
                     +LIRPSGTEP IRV+AE
Sbjct: 409 ----------LLIRPSGTEPLIRVMAE 425


Lambda     K      H
   0.318    0.138    0.402 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 491
Number of extensions: 28
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 450
Length of database: 450
Length adjustment: 33
Effective length of query: 417
Effective length of database: 417
Effective search space:   173889
Effective search space used:   173889
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory